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| Status |
Public on Oct 03, 2023 |
| Title |
Bulk RNA-seq of sorted CD4 T cells from CSF of a third person living with FBSS |
| Sample type |
SRA |
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| Source name |
Cerebrospinal Fluid
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Cerebrospinal Fluid
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For bulk sequencing,lysed cells were directly amplified into double stranded cDNA using the SMARTer protocol as described elsewhere (Picelli et al., 2014). All three cell types (CD4+ T cells, CD8+ T cells and monocytes) derived from one individual would be amplified at once. For single cell sequencing, we used a 10X Chromium Platform following manufacturer's protocols.
For bulk sequencing, library preparation from cDNA and sequencing were performed by an external company (Genewiz). For CITE-sequencing, the King's BRC Genomics facility followed the workflow recommended by 10X.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
X013_FBSS_CD4T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx
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| Data processing |
Bulk sequencing reads were pseudo-aligned with kallisto version 0.48.0 to the human genome: Homo Sapiens GCRh38, kallisto index version 10 (Bray et al., 2016).
Differential expression analyses were performed using DESeq2 (Love et al., 2014) or limma (Ritchie et al., 2015) in R.
CITE-sequencing reads were aligned using 10X Genomics CellRanger.
CITE-seq data were further processed using the R package Seurat (Hao et al., 2021).
Other packages we used were: SingleR (Aran et al., 2019) and SingleCellExperiment (Amezquita et al., 2020).
Assembly: Homo Sapiens GCRh38
Supplementary files format and content: Seurat objects are provided for single cell data. Please see manuscript for detailed descriptions.
Supplementary files format and content: Excel files are provided for bulk sequencing data. Please see manuscript for detailed descriptions.
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| Submission date |
Oct 02, 2023 |
| Last update date |
Oct 03, 2023 |
| Contact name |
Franziska Denk |
| Organization name |
King's College London
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| Department |
Wolfson SPaRC
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| Street address |
Guy's Campus
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| City |
London |
| ZIP/Postal code |
SE1 1UL |
| Country |
United Kingdom |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE244499 |
Cerebrospinal fluid immune cells appear similar across neuropathic and non-neuropathic pain conditions. |
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| Relations |
| BioSample |
SAMN37651255 |
| SRA |
SRX21970847 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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